Russell Turner, Ph.D.

3709 Takoya Drive, Ellicott City, MD 21042
phone: 410-203-0260    http://www.umbc.edu/~turner    mailto: turner@umbc.edu

Curriculum Vitae

Summary

Senior computer scientist with experience as a programmer, team manager, software development technical lead, researcher and teacher. Knowledgeable in the areas of bioinformatics visualization, object-oriented design,  interactive 2D and 3D graphics, 3D character animation and GUI toolkit design. Strong Java and C/C++ programming experience, with responsibility for full life-cycle design and development of several large Java-based commercial graphics products, including three-tiered applications for visualizing and annotating bioinformatics data. Ph.D. in computer animation, with academic research experience.

Skills

Employment

• Comparative Genomics Viewer:
Designed and implemented Atavist, an interactive Java-based research tool for viewing and analyzing comparative genomics data. Displays multiple genomic axes together with aligned genomic features and syntenic relationships.
• Comparative Feature Projection Tool:
Designed and implemented Atalanta, a Unix tool written in C++ to project genomic feature coordinates between different genome assemblies of the same or closely related species. Used as a component in the AIR pipeline for computing gene annotations on Celera’s Rat genome sequence. Projections are based on assembly-to-assembly mapping data generated by the ATAC mapping tool.
• LCMS Spectrum Viewer:
Developed prototype tool for viewing liquid chromatography mass spectrometry data. Displays data as a 3D height field with interactive pan and zoom capabilities. Data is loaded in progressively from a hierarchically formatted file as user zooms in, allowing large datasets to be viewed on small memory machines. Written in Java using the Swing and VTK graphics packages.

• Mass Spectrometry Visualization Application:
Responsible for full life-cycle design and development of the MSMSViewer, an interactive Java-based 3-tiered application for viewing and curating tandem mass spectrometry data from Celera’s proteomics pipeline. It consists of a front-end based on Swing and Sitraka JChart graphics APIs, an EJB-based middle tier running in a JBoss application server, and an Oracle database backend. Developed using JDK1.3, JBuilder and MagicDraw development tools.

• Genome Annotation Application:
Technical lead responsible for designing and developing the Celera Genome Browser, an interactive Java-based 3-tiered application used by Celera scientists and customers for visualizing and annotating genomic data, including Celera’s human genome database. The front-end is a high-performance "thick" client which loads serialized Java objects on demand from an EJB-based middle tier running in a WebLogic application server, hitting an Oracle database backend. The client is constructed using a standard MVC software architecture, and users can integrate their own data with the database data by loading XML files into the client model. Annotation is performed via interactive "drag and drop" creation and editing of annotation features with infinite-level undo. Developed using JDK1.3, Jbuilder and TogetherJ development tools.

• Java Dynamic Drawing Editor Product:
Concept, design, major implementation and documentation of JGraphics, a Java-based visual software development system for building interactive data-driven dynamic graphics displays with little or no programming. Utilizes interactive iconic programming methodology similar to JavaStudio. Displays can run as web applets, standalone applications or JavaBeans. Developed on Windows and Linux platforms using JDK1.1, Symantec Café and JBuilder development tools. Full hierarchical vector graphics functionality built on top of AWT drawing model. Dynamics implemented by specialized dataflow propagation algorithm incorporating lazy evaluation. Imports and exports JavaBeans with data connectivity to sockets and JDBC via SQL.

• Virtual Reality Toolkit:
Principal Investigator, co-designer and supervisor of four research assistants for Metis, a research object-oriented toolkit for implementing 3D interactive simulations, sponsored by an NSF grant. Toolkit employs a client/server architecture with an API on the server side communicating via TCP/IP Sockets with a client viewer program that handles all immersive display and interactivity. Implemented in C++ using X11/Motif and OpenGL on a Silicon Graphics Reality Engine platform.

• Image Understanding Toolkit:
Designed and implemented early prototypes for the graphical user interface portion of the Image Understanding Environment, a DARPA-sponsored object-oriented toolkit for image understanding. Implemented in C++ using the X11/Motif GUI toolkit.

• Deformable Character Animation System:
Designed and implemented LEMAN research animation system, which allows deformable 3D layered cartoon characters to be constructed and animated in an interactive, direct-manipulation environment. The skin layer is implemented as a real-time physical simulation of an elastic surface which is constrained to an underlying articulated figure using force-based constraints. The underlying skeleton is positioned interactively using inverse kinematics and animated using key joint-angle interpolation. Implemented in C using IrisGL on a Silicon Graphics platform.

• 3D GUI Toolkit:
Member of development team of four research assistants designing and implementing the Fifth Dimension Toolkit, a research software library for building animation systems and 3D interactive environments on Silicon Graphics Iris and Next workstations. Implements a traditional 2D widget set integrated with a set of 3D graphical classes, non-conventional input device classes, and a network interface to a MIDI environment. It was designed using object-oriented software construction principles and implemented in C, Objective-C and Eiffel using IrisGL and NextStep graphics APIs.

Education

• Dissertation:
Interactive Construction and Animation of Layered Elastic Characters. Presents the elastic surface layer model, for simulating deformable 3D animated characters, and the LEMAN research animation system for studying interactive layered character construction and animation techniques. Daniel Thalmann, advisor.

• Master's Project:
A Ray-Traced Image Generator for the Edinburgh Designer System. Unix application in C for generation of realistic color images using ray-tracing. Models are specified with constructive solid geometry using an original modeling language. Robin Popplestone, advisor.

Research Interests

Research Grants

• An Object-Oriented 3D Interaction Toolkit for Virtual Environment Research,
NSF (1995-98)
• Head-Tracked Stereo Viewing and Direct-Manipulation 3D Interaction Techniques for Volumetric Visualization of CT Scan Data
(Johns Hopkins University, Summer 1996)
• A Virtual Human Sculpture System,
UMBC Designated Research Initiative Fund (1995-96)

Courses Developed and Taught

• Introduction to Computer Science I
(in C)
• Graphical User Interface Programming
(with Java, Motif and OpenGL)
• Data Structures
(in C++)
• Animation and 3D Graphics
(seminar)
• Virtual Environments
(seminar)

Publications and Presentations

1. Florea L, et al (2004) Gene and Alternative Splicing Annotation with AIR (Submitted for publication).
2. Istrail S, Sutton GG, Florea L, et al (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1916-21. Epub 2004 Feb 09.
3. Turner RJ (2002) The Celera Genome Browser: A Tool for Visualizing and Annotating the Human Genome Bio-Informatics Visualization Workshop Presented on May 30, 2002, Human-Computer Interaction Lab, University of Maryland, College Park.
4. Turner RJ, et al (2001) Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm. Proceedings of the IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics pp. 7-18, October 22-23, 2001, ACM SIGGRAPH, IEEE 01EX520, ISBN 0-7803-7223-9.
5. Venter JC, Adams MD, Myers EW, et al (2001) The sequence of the human genome. Science 291, pp1145-1434.
6. Adams, MD et al (2000) The Genome Sequence of Drosophila melanogaster. Science 287 pp2185-2195
7. Turner R, Song L, Gobbetti E. (1999) Metis: An Object-Oriented Toolkit for Constructing Virtual Reality Applications. Computer Graphics Forum, 18(2): 121-131, June 1999.
8. Turner R, Gobbetti E (1998) Interactive Construction and Animation of Layered Elastically Deformable Characters. Computer Graphics Forum, 17(2):135-152, June 1998.
9. Turner R, Gobbetti E, Soboroff I, (1996) Head-Tracked Stereo Viewing with Two-Handed 3D Interaction for Animated Character Construction. Computer Graphics Forum, 15(3): 197-206, 470, September 1996. Proceedings of the 1996 17th Annual Conference and Exhibition of the European Association for Computer Graphics, Eurographics'96, held in Poitiers, France.
10. Gobbetti E, Turner R, (1997) Exploring Annotated 3D Environments on the World-Wide Web using VRML In Jim Mayfield and Charles Nicholas, editors, Intelligent Hypertext: Advanced Techniques for the World-Wide Web. Volume 1326 of Lecture Notes in Computer Science. Pages 31-46, Springer-Verlag Inc., New York, NY, USA, 1997.
11. Turner R, (1995) LEMAN: A System For Constructing and Animating Layered Elastic Characters. Computer Graphics: Developments in Virtual Environments, R. A. Earnshaw and J. A. Vince (Eds.), Proceedings of CGI 95, Leeds, England, pp 185-203, Academic Press, San Diego, CA, June 1995.
12. Turner R, Thalmann D. (1993) The Elastic Surface Layer Model for Animated Character Construction. Proceedings of CG International, Lausanne, Switzerland. Pages 399-412, Springer-Verlag 1993.
13. Gobbetti E, Balaguer F, Mangili A, Turner R, (1993) Building an Interactive 3D Animation System, In Bertrand Meyer and Jean-Marc Nerson, editors, Object-Oriented Applications. Pages 211-242, Prentice-Hall, Englewood Cliffs, NJ 07632, USA, 1993.
14. Turner R, Gobbetti E, Balaguer F, Thalmann D. (1991) Physically-Based Interactive Camera Control Using 3D Input Devices, In N. M. Patrikalakis, editor, Scientific Visualization of Physical Phenomena: Proceedings of CG International Tokyo. Pages 135-145. Springer-Verlag Inc., 1991.
15. LeBlanc A, Turner R, Thalmann D. (1991) Rendering Hair using Pixel Blending and Shadow Buffers. Journal of Visualization and Computer Animation Vol. 2, No. 3, 1991, pp 92-97, John Wiley.
16. Gobbetti E, Turner R. (1991) Object-Oriented Design of Dynamic Graphics Applications, in Daniel Thalmann and Nadia Magnenat-Thalmann, editors, New Trends in Animation and Visualization.. Pages 43-58, Wiley, New York, NY, USA, 1992.
17. Turner R, Gobbetti E, Balaguer F, Mangili A, Thalmann D, Magnenat-Thalmann N. (1990) An Object Oriented Methodology Using Dynamic Variables for Animation and Scientific Visualization, in Proceedings Computer Graphics International. Pages 317-328. Springer-Verlag Inc., 1990.

Other Interests